Main
Ruth Lydia Schmidt
Microbial Ecologist & Data Scientist
A dynamic and resourceful microbial ecologist with 8 years of experience in
agricultural microbiome research, data analysis and science communication, strong leadership and a broad set of technical and interpersonal skills.
Passionate about finding sustainable solutions for pressing issues of our time through science, data and policy.
Education
Ph.D. in Microbial Ecology
Wageningen University & Netherlands Institute of Ecology
Title: Volatile communication between fungi and bacteria
Wageningen, The Netherlands
2017
M.S. in Biotechnology
Graz University of Technology
Graz, Austria
2012
M.S. in Molecular Biology
Graz University of Technology
Graz, Austria
2010
Research Experience
Mitacs Postdoctoral Fellow
Institut national de la recherche scientifique (INRS) & Plotly
Montréal, Canada
2020 - Present
- Developing open-source visualization apps for omic data in microbiome research using Ploty’s Dash R and Dash Bio libraries.
Visiting JSPS Postdoctoral Fellow (short-term stay)
Kochi Core Center
Kochi, Japan
2020
- Developed screening method for detection of terpene synthase genes (TPS) across terrestrial and aquatic environments.
Consultant
International Union for Conservation of Nature (IUCN)
remote
2019
- Contributed to a global report on soil biodiversity in agro-ecosystem health.
Postdoctoral Fellow
Institut national de la recherche scientifique (INRS)
Montréal, Canada
2018 - 2020
- Research on microbial solutions to drought in agriculture.
- Led lab and field studies with wheat under drought conditions.
- Conducted analysis of omic data (quantitative metagenomics, metatranscriptomics, metabolomics).
PhD Candidate
Netherlands Institute of Ecology & Wageningen University
Wageningen, The Netherlands
2013 - 2018
- Studied microbial secondary metabolites for sustainable agriculture.
- Characterized molecular mechanism underlying volatile interaction in soil microbes using a combination of omic, microbiological, and analytical (GC-MS) approaches.
- Analyzed omic data (proteomics, metabolomics) and developed workflow for metabolomic data analysis.
- Mentored 4 undergraduate and 1 graduate student on molecular biology research projects.
- Collaborated with international research institutes in Germany, US & Sweden on genomics and proteomics projects.
Master student and University assistant
Graz University of Technology
Graz, Austria
2010-2012
- Led and conducted field study on the effect of biocontrol agents in field in Egypt.
- Performed analysis of 16S rRNA sequencing data & analytical data (LC-MS).
Teaching Experience
Supervisor of 2 PhD and 2 master students
Institut national de la recherche scientifique (INRS)
Montréal, Canada
2018 - Present
Teaching Assistant in Microbial Ecology field course
Wageningen University
Wageningen, The Netherlands
2016
Instructor in two days hands-on course on environmental proteomics
Netherlands Institute of Ecology
Wageningen, The Netherlands
2016
Supervisor of 3 Bachelor, 2 Master student & 1 PhD student
Wageningen University
Wageningen, The Netherlands
2014 - 2017
Teaching Assistant in Laboratory Course Environmental and Food Biotechnology
Graz University of Technology
Graz, Austria
2013
Research Assistant in Laboratory Course in Biochemistry and Molecular Biology
Karl-Franzens University
Graz, Austria
2012
Grants & awards
Mitacs Postdoctoral Fellowship (60,000 CAD)
Visualization of multi-omics data in microbiome research
Montréal, Canada
2019
Japan Society for the Promotion of Science (JSPS) Award (8,000 CAD)
Uncovering microbial chemical ecology in the extreme sub-seafloor environment
Kochi Core Centre, Japan
2019
Quebec Centre for Biodiversity Science (QCBS) Travel grant (1,500 CAD)
International Phytobiome meeting
Montpellier, France
2018
QCBS Seed grant (5,000 CAD)
Aural soilscapes: creating ecological consciousness to global warming
Montréal, Canada
2018
QCBS Travel grant (1,500 CAD)
ISME17 meeting
Leipzig, Germany
2018
International Society of Chemical Ecology (ISCE) Travel Grant (1,000 USD)
Annual Meeting ISCE17
Kyoto, Japan
2017
Best Talk Award (150 USD)
Annual Meeting ISCE17
Kyoto, Japan
2017
Federation of European Microbiological Societies (FEMS) Research Grant (5,000 Eur)
Research on fungal genomics at the Swedish University of Agricultural Sciences (SLU)
Uppsala, Sweden
2017
International Society for Microbial Ecology (ISME) Travel Grant (800 Eur)
ISME16 meeting
Montréal, Canada
2016
FEMS Meetings Attendance Grant (300 Eur)
Ecology of Soil Microorganisms meeting
Prague, Czech Republic
2015
Best Poster Award (100 Eur)
Ecology of Soil Microorganisms meting
Prague, Czech Republic
2015
Presentations
Kochi Core Center (talk)
Uncovering microbial terpenes in the extreme sub-seafloor environment.
Kochi, Japan
2020
International Society of Chemical Ecology, ISCE 35 (talk)
Microbial chemical ecology: past, present and future.
Atlanta, USA
2019
Second International Holobiont meeting (talk)
How microbial volatiles help plants survive in times of drought.
Montréal, Canada
2019
QCBS Symposium (talk)
Microbial aromas might help plants survive drought.
Montréal, Canada
2018
International Phytobiome meeting (poster)
Microbial terpenes in the plant holobiont as a mechanism to adapt to drought.
Montpellier, France
2018
International Symposium on Microbial Ecology, ISME 17 (talk)
Do bacteria and fungi have a fragrant language all their own?
Leipzig, Germany
2018
Champalimaud Centre for the Unknown
Microworld - the most powerful life on earth.
Lisbon, Portugal
2018
International Society of Chemical Ecology, ISCE 17 (talk)
Terpenes as lingua franca between fungi and bacteria.
Kyoto, Japan
2017
International Symposium on Microbial Ecology, ISME 16 (poster)
Volatile conversations between fungi and bacteria.
Montréal, Canada
2016
Ecology of soil microorganisms, ESM (poster)
Microbial small talk: Volatiles in fungal-bacterial interactions.
Prague, Czech Republic
2015
4th International student conference on Microbial Communication, MiCom (talk)
Chemical dialogues: The ability of bacteria to sense fungal volatiles.
Jena, Germany
2014
CNRS-Jacques Monod conference: bacterial–fungal interactions: a federative field for fundamental and applied microbiology
The role of fungal volatiles as signaling compounds in bacterial-fungal interactions.
Roscoff, France
2013
Boston Bacterial Meeting, BBM (poster)
Microbial interactions via secondary metabolites in soil.
Boston, USA
2013
Netherlands Annual Ecology Meeting, NERN (poster)
The best bacterial competitive strategies in the rhizosphere.
Lunteren, The Netherlands
2013
Publications
A Gaseous Milieu: Extending the Boundaries of the Rhizosphere.
Trends in microbiology. DOI: 10.1016/j.tim.2020.02.016
N/A
2020
de la Porte, A., Schmidt, R., Yergeau, É., & Constant, P.
Microbe-driven chemical ecology: past, present and future.
ISME J. DOI: 10.1038/s41396-019-0469-x
N/A
2019
Schmidt, R., Ulanova, D., Wick, L. Y., Bode, H. B., & Garbeva, P.
Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum.
FEMS Microbiol Ecol. DOI: 10.1093/femsec/fiy078
N/A
2018
Schmidt, R., Durling, M. B., de Jager, V., Menezes, R. C., Nordkvist, E., Svatoš, A., Dubey, M., Lauterbach, L., Dickschat, J. S., Karlsson, M., & Garbeva, P.
Fifty Percent Human - how art brings us in touch with our microbial cohabitants.
Microb Biotechnol.DOI: 10.1111/1751-7915.13285
N/A
2018
Bäumel, S., Tytgat, H., Nemec, B., Schmidt, R., Chia, L. W., & Smidt, H.
The future of ecology is collaborative, inclusive and deconstructs biases.
Nat Ecol Evol. DOI: 10.1038/s41559-017-0445-7
N/A
2018
Ramirez, K. S., Berhe, A. A., Burt, J., Gil-Romera, G., Johnson, R. F., Koltz, A. M., Lacher, I., McGlynn, T., Nielsen, K. J., Schmidt, R., Simonis, J. L., terHorst, C. P., & Tuff, K. Scientific reports.
Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI-2C.
Sci Rep. DOI: 10.1038/s41598-017-00893-3
N/A
2017
Schmidt, R., Jager, V., Zühlke, D., Wolff, C., Bernhardt, J., Cankar, K., Beekwilder, J., Ijcken, W. V., Sleutels, F., Boer, W., Riedel, K., & Garbeva, P.
Controlling the Microbiome: Microhabitat Adjustments for Successful Biocontrol Strategies in Soil and Human Gut.
Front Microbiol. DOI: 10.3389/fmicb.2016.01079
N/A
2016
Adam, E., Groenenboom, A. E., Kurm, V., Rajewska, M., Schmidt, R., Tyc, O., Weidner, S., Berg, G., de Boer, W., & Falcão Salles, J.
Microbial Small Talk: Volatiles in Fungal-Bacterial Interactions.
Front Microbiol. DOI: 10.3389/fmicb.2015.01495
N/A
2016
Schmidt, R., Etalo, D. W., de Jager, V., Gerards, S., Zweers, H., de Boer, W., & Garbeva, P.
Volatile affairs in microbial interactions.
ISME J. DOI: 10.1038/ismej.2015.42
N/A
2016
Schmidt, R., Cordovez, V., de Boer, W., Raaijmakers, J., & Garbeva, P.
Exploring the genomic traits of fungus-feeding bacterial genus Collimonas.
BMC Genomics. DOI: 10.1186/s12864-015-2289-3
N/A
2015
Song, C., Schmidt, R., de Jager, V., Krzyzanowska, D., Jongedijk, E., Cankar, K., Beekwilder, J., van Veen, A., de Boer, W., van Veen, J. A., & Garbeva, P.
Effects of bacterial inoculants on the indigenous microbiome and secondary metabolites of chamomile plants.
Front Microbiol. DOI: 10.3389/fmicb.2013.00400
N/A
2014
Schmidt, R., Köberl, M., Mostafa, A., Ramadan, E. M., Monschein, M., Jensen, K. B., Bauer, R., & Berg, G.
The microbiome of medicinal plants: diversity and importance for plant growth, quality and health.
Front Microbiol. DOI: 10.3389/fmicb.2014.00064
N/A
2013
Köberl, M., Schmidt, R., Ramadan, E. M., Bauer, R., & Berg, G.
Manuscripts in preparation
Soil hydrogen enrichment increases H2-oxiding bacterial activity and changes microbial community structure and function (under review).
Soil Biol. Biochem.
N/A
N/A
Wang X., Schmidt R., Constant P., & Yergeau E.
Nitrapyrin has far reaching effects on the soil microbial community structure, composition, diversity and functions (submitted).
Appl. Environ. Microbiol.
N/A
N/A
Schmidt R., Wang X., Garbeva, P., & Yergeau E.
Infochemicals in terrestrial plants and marine macroalgal holobionts under a changing climate (under review).
New Phytologist.
N/A
N/A
Schmidt R., & Saha, M.